3AF8

Crystal Structure of Pd(ally)/apo-C126AFr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes into the Protein Nanocage of apo-Ferritin.

Abe, S.Hikage, T.Watanabe, Y.Kitagawa, S.Ueno, T.

(2010) Inorg.Chem. 49: 6967-6973

  • DOI: 10.1021/ic1003758
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hybridization of metal complexes and protein scaffolds is an important subject in bioinorganic chemistry and materials science. Efforts to provide non-natural functions to proteins will likely lead to advances in development of catalysts, sensors, an ...

    Hybridization of metal complexes and protein scaffolds is an important subject in bioinorganic chemistry and materials science. Efforts to provide non-natural functions to proteins will likely lead to advances in development of catalysts, sensors, and so on. Mechanistic investigations of the process of binding of metal complexes within protein scaffolds and characterization of the resulting coordination structures will help us to design and control coordination structures of metal complexes for construction of hybrid proteins containing metal complexes. In this work, the processes of accumulation and incorporation of organometallic palladium complexes within the cage of the iron storage protein apo-ferritin (apo-Fr) are elucidated by analysis of X-ray crystal structures of apo-Fr and selected mutants thereof, in the presence of the metal complexes. The crystal structure of apo-Fr containing Pd(allyl) (allyl = eta(3)-C(3)H(5)) complexes shows that thiolato-bridged dinuclear Pd(allyl) complexes are formed at two binding sites within the cage of apo-Fr. The crystal structures of apo-Fr and its Cys- and His-deletion mutants containing Pd(allyl) complexes indicate that Cys126 accelerates the incorporation of Pd(allyl) complexes into the cage. In addition, Cys48 and Cys126 are essential for accumulation of Pd(allyl) complexes and stabilizing the square planar coordination structure.


    Organizational Affiliation

    Institute for Integrated Cell-Material Sciences (iCeMS), Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferritin light chain
X
174Equus caballusMutation(s): 1 
Gene Names: FTL
Find proteins for P02791 (Equus caballus)
Go to Gene View: FTL
Go to UniProtKB:  P02791
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
X
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PLL
Query on PLL

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Download CCD File 
X
Palladium(II) allyl complex
C3 H5 Pd
WTWGCTVOVPTEEU-CPNWEVAQAE
 Ligand Interaction
CD
Query on CD

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Download CCD File 
X
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.181 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 181.984α = 90.00
b = 181.984β = 90.00
c = 181.984γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance